Transcriptome analysis reveals self-incompatibility in the tea plant (Camellia sinensis) might be under gametophytic control

Abstract

BackgroundSelf-incompatibility (SI) is under genetic control and prevents inbreeding depression in angiosperms. SI mechanisms are quite complicated and still poorly understood in many plants. Tea (Camellia sinensis L.) belonging to the family of Theaceae, exhibits high levels of SI and high heterozygosity. Uncovering the molecular basis of SI of the tea plant may enhance breeding and simplify genomics research for the whole family.ResultsThe growth of pollen tubes following selfing and crossing was observed using fluorescence microscopy. Self-pollen tubes grew slower than cross treatments from 24 h to 72 h after pollination. RNA-seq was employed to explore the molecular mechanisms of SI and to identify SI-related genes in C. sinensis. Self and cross-pollinated styles were collected at 24 h, 48 h and 72 h after pollination. Six RNA-seq libraries (SP24, SP48, SP72, CP24 CP48 and CP72; SP = self-pollinated, CP = cross-pollinated) were constructed and separately sequenced. In total, 299.327 million raw reads were generated. Following assembly, 63,762 unigenes were identified, and 27,264 (42.76 %) unigenes were annotated in five public databases: NR, KOG, KEGG, Swiss-Port and GO. To identify SI-related genes, the fragments per kb per million mapped reads (FPKM) values of each unigene were evaluated. Comparisons of CP24 vs. SP24, CP48 vs. SP48 and CP72 vs. SP72 revealed differential expression of 3,182, 3,575 and 3,709 genes, respectively. Consequently, several ubiquitin-mediated proteolysis, Ca2+ signaling, apoptosis and defense-associated genes were obtained. The temporal expression pattern of genes following CP and SP was analyzed; 6 peroxidase, 1 polyphenol oxidase and 7 salicylic acid biosynthetic process-related genes were identified. The RNA-seq data were validated by qRT-PCR of 15 unigenes. Finally, a unigene (CL25983Contig1) with strong homology to the S-RNase was analyzed. It was mainly expressed in styles, with dramatically higher expression in self-pollinated versus cross-pollinated tissues at 24 h post-pollination.ConclusionsThe present study reports the transcriptome of styles after cross- and self-pollination in tea and offers novel insights into the molecular mechanism behind SI in C. sinensis. We believe that this RNA-seq dataset will be useful for improvement in C. sinensis as well as other plants in the Theaceae family.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2703-5) contains supplementary material, which is available to authorized users.

Gene expression analysis of bud and leaf color in tea

“…Finally, short reads were assembled into 112,233 unigenes, with an average length of 759 bp and N50 length of 1081 bp (Table S2). The assembled unigenes obtained by RNA-Seq analysis in C. sinensis showed a large variation according to present studies, which ranged from 63,762 to 347,827 Shi et al, 2015;Tai et al, 2015;Zhang et al, 2016). The variation might be associated with sequencing depth, software for assemble and tissues used for experiments (Cai et al, 2012).…”

“…Recently, RNA-Seq method of high-throughput sequencing technology has been widely used to explore the potential mechanisms associated with important traits in C. sinensis (Paul et al, 2014;Li et al, 2015;Shi et al, 2015;Tai et al, 2015;Wei et al, 2015;Wang et al, 2016;Wu et al, 2016;Zhang et al, 2016). This method allows a comparison of the whole transcriptome of samples with large difference in certain trait or under treatments.…”

In-Depth Understanding of Camellia oleifera Self-Incompatibility by Comparative Transcriptome, Proteome and Metabolome

“…The knowledge of specifically or preferentially expressed genes of self-ovules (the ovule after self-pollination) is a valuable resource for genetic analyses of candidate genes involved in the LSI response; for example, Zhou and Zheng found that signal transduction-related genes and specifically expressed transcription factors might be involved in self-incompatible reactions in Xanthoceras sorbifolium [29]. Another study reported the transcriptome of styles after cross-and self-pollination and offered novel insights into the molecular mechanism of LSI in Camellia sinensis [30,31]. It was found that a single gene (CL25983Contig1) had high homology with S-RNase and was expressed at a significantly higher level 24 h after pollination in a self-pollinated plant than that in the cross-pollinated group [30].…”

“…Another study reported the transcriptome of styles after cross-and self-pollination and offered novel insights into the molecular mechanism of LSI in Camellia sinensis [30,31]. It was found that a single gene (CL25983Contig1) had high homology with S-RNase and was expressed at a significantly higher level 24 h after pollination in a self-pollinated plant than that in the cross-pollinated group [30]. Lanaud et al used GWAS to screen loci associated with Theobroma cacao LSI and identified two loci located on chromosomes 1 and 4 that were closely related to the LSI reaction [32].…”

Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology

“…SI in tea is not fully characterized but self-pollen rejection has been detected at the ovary consistent with LSI systems. According to Zhang et al (2016), transcriptome analysis of self/crosspollinated styles permitted identification of a differentially expressed gene (DEG) highly homologous to S-RNase. However, in a similar study, Ma et al (2018) did not find S-RNase homologs, but instead identified other DEGs (e.g., aGtype LecRLK).…”